BtaINT0053823 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015991 | E-CADHERIN
Description
Bos taurus cadherin 1, type 1, E-cadherin (epithelial) (CDH1), mRNA. [Source:RefSeq mRNA;Acc:NM_001002763]
Coordinates
chr18:36239123-36239900:+
Coord C1 exon
chr18:36239123-36239347
Coord A exon
chr18:36239348-36239669
Coord C2 exon
chr18:36239670-36239900
Length
322 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGC
5' ss Score
7.93
3' ss Seq
ATTTTTGTTGCTTCCTCCAGAAC
3' ss Score
9.44
Exon sequences
Seq C1 exon
GTTCTCCACCTGCCACTGGGACAGGCACCCTGCTCTTGTTCCTCGATGATGTGAATGACAATGGCCCCGTACCAGAACCCCGGACCATGGACTTCTGCCAGAGGAATCCTGAGCCTCACATCATCAACATCAATGATCCTGATCTCCCTCCGAACACCTCCCCCTTTACAGCAGAACTGACACATGGGGCGAGTGTCAATTGGACCATTGAGTACAATGACCAAG
Seq A exon
GTGGGCACCAGAGCCTTTCTTATTTTGGAAACTTTGCTCTGACCCTCTGCTTCCCCTCCCCTGCCCTTCTGAATTTCGCTTCTCAGTATCCACTTGTCACTCCTTTTAAGGTATGTTTCCTGGTCCCTTCTACATTTGTGACATTGAACCAAAGGTCCTTTTGTGTTTCTCGCATCTTAGTCTGTGACATGCTGCCTATTAAGCTGCAGCTCAAATAGTTGTCATCTTCACTTGGTTTTGGAATGTCTCTAGTTCCTTAATCAGTTTAGTCTGGAATGAACTTTTTCTCTTCCAATCCCCTCATTTTTGTTGCTTCCTCCAG
Seq C2 exon
AACGTGAGTCTCTGATTTTGAAGCCAAAGAAAACCTTAGAGCTGGGTGACCACAAAATCAATCTCAAGCTCATAGACAACCAGAACAAAGACCAGGTGACCACACTTGATGTGCACGTGTGTGACTGTGATGGGATCGTCAGCAACTGCAGGAAGGCCACGGCCTTTGCTGAAGCAGGATTGCAAGTTCCCGCCATCCTGGGGATCCTCGGAGGCATCCTTGCTTTTCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015991:ENSBTAT00000021272:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.566 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(14.7=18.4),PF0002812=Cadherin=PU(53.9=63.2)
A:
NA
C2:
PF0002812=Cadherin=PD(44.9=51.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCCTGCTCTTGTTCCTCGAT
R:
CTTCCTGCAGTTGCTGACGAT
Band lengths:
354-676
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development